2CNP

HIGH RESOLUTION SOLUTION STRUCTURE OF APO RABBIT CALCYCLIN, NMR, 22 STRUCTURES


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 112 
  • Conformers Submitted: 22 
  • Selection Criteria: DEFINED THE MINIMAL NUMBER OF CONFORMERS NEEDED TO REPRESENT THE SRUCTURE. THE MEMBERS OF THE ENSEMBLE WERE CHOSEN BASED ON A COMBINATION OF LEAST RESTRAINT VIOLATION ENERGY AND MOLECULAR ENERGIES. 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High resolution solution structure of apo calcyclin and structural variations in the S100 family of calcium-binding proteins.

Maler, L.Potts, B.C.Chazin, W.J.

(1999) J.Biomol.NMR 13: 233-247


  • PubMed Abstract: 
  • The three-dimensional solution structure of apo rabbit lung calcyclin has been refined to high resolution through the use of heteronuclear NMR spectroscopy and 13C, 15N-enriched protein. Upon completing the assignment of virtually all of the 15N, 13C ...

    The three-dimensional solution structure of apo rabbit lung calcyclin has been refined to high resolution through the use of heteronuclear NMR spectroscopy and 13C, 15N-enriched protein. Upon completing the assignment of virtually all of the 15N, 13C and 1H NMR resonances, the solution structure was determined from a combination of 2814 NOE-derived distance constraints, and 272 torsion angle constraints derived from scalar couplings. A large number of critical inter-subunit NOEs (386) were identified from 13C-select, 13C-filtered NOESY experiments, providing a highly accurate dimer interface. The combination of distance geometry and restrained molecular dynamics calculations yielded structures with excellent agreement with the experimental data and high precision (rmsd from the mean for the backbone atoms in the eight helices: 0.33 A). Calcyclin exhibits a symmetric dimeric fold of two identical 90 amino acid subunits, characteristic of the S100 subfamily of EF-hand Ca(2+)-binding proteins. The structure reveals a readily identified pair of putative sites for binding of Zn2+. In order to accurately determine the structural features that differentiate the various S100 proteins, distance difference matrices and contact maps were calculated for the NMR structural ensembles of apo calcyclin and rat and bovine S100B. These data show that the most significant variations among the structures are in the positioning of helix III and in loops, the regions with least sequence similarity. Inter-helical angles and distance differences for the proteins show that the positioning of helix III of calcyclin is most similar to that of bovine S100B, but that the helix interfaces are more closely packed in calcyclin than in either S100B structure. Surprisingly large differences were found in the positioning of helix III in the two S100B structures, despite there being only four non-identical residues, suggesting that one or both of the S100B structures requires further refinement.


    Related Citations: 
    • A Calcium-Binding Protein from Rabbit Lung Cytosol Identified as the Product of Growth-Regulated Gene (2A9) and its Binding Proteins
      Tokumitsu, H.,Kobayashi, R.,Hidaka, H.
      (1995) Arch.Biochem.Biophys. 291: 401
    • 1H NMR Assignments of Apo Calcyclin and Comparative Structural Analysis with Calbindin D9K and S100 Beta
      Potts, B.C.,Carlstrom, G.,Okazaki, K.,Hidaka, H.,Chazin, W.J.
      (1996) Protein Sci. 5: 2162
    • Erratum. The Structure of Calcyclin Reveals a Novel Homodimeric Fold for S100 Ca(2+)-Binding Proteins
      Potts, B.C.,Smith, J.,Akke, M.,Macke, T.J.,Okazaki, K.,Hidaka, H.,Case, D.A.,Chazin, W.J.
      (1995) Nat.Struct.Mol.Biol. 2: 912
    • The Structure of Calcyclin Reveals a Novel Homodimeric Fold for S100 Ca(2+)-Binding Proteins
      Potts, B.C.,Smith, J.,Akke, M.,Macke, T.J.,Okazaki, K.,Hidaka, H.,Case, D.A.,Chazin, W.J.
      (1995) Nat.Struct.Mol.Biol. 2: 790
    • A Calcium-Binding Protein from Rabbit Lung Cytosol Identified as the Product of Growth-Regulated Gene (2A9) and its Binding Proteins
      Tokumitsu, H.,Kobayashi, R.,Hidaka, H.
      (1991) Arch.Biochem.Biophys. 288: 202


    Organizational Affiliation

    Department of Molecular Biology (MB9), Scripps Research Institute, La Jolla, CA 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CALCYCLIN
A, B
90Oryctolagus cuniculusMutation(s): 0 
Gene Names: S100A6
Find proteins for P30801 (Oryctolagus cuniculus)
Go to Gene View: S100A6
Go to UniProtKB:  P30801
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 112 
  • Conformers Submitted: 22 
  • Selection Criteria: DEFINED THE MINIMAL NUMBER OF CONFORMERS NEEDED TO REPRESENT THE SRUCTURE. THE MEMBERS OF THE ENSEMBLE WERE CHOSEN BASED ON A COMBINATION OF LEAST RESTRAINT VIOLATION ENERGY AND MOLECULAR ENERGIES. 
  • Olderado: 2CNP Olderado
Software Package:
Software NamePurpose
AMBERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-07-22
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance